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- PDB-6n4y: Metabotropic Glutamate Receptor 5 Extracellular Domain with Nb43 -

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Basic information

Entry
Database: PDB / ID: 6n4y
TitleMetabotropic Glutamate Receptor 5 Extracellular Domain with Nb43
Components
  • Metabotropic glutamate receptor 5
  • Nanobody 43Single-domain antibody
KeywordsMEMBRANE PROTEIN / Cell Surface Receptor Nanobody
Function / homologyGPCR, family 3, conserved site / Homer-binding domain of metabotropic glutamate receptor / Periplasmic binding protein-like I / Metabotropic glutamate receptor, Homer-binding domain / GPCR, family 3, metabotropic glutamate receptor / Receptor family ligand binding region / Nine Cysteines Domain of family 3 GPCR / GPCR, family 3, metabotropic glutamate receptor 5 / GPCR, family 3 / Receptor, ligand binding region ...GPCR, family 3, conserved site / Homer-binding domain of metabotropic glutamate receptor / Periplasmic binding protein-like I / Metabotropic glutamate receptor, Homer-binding domain / GPCR, family 3, metabotropic glutamate receptor / Receptor family ligand binding region / Nine Cysteines Domain of family 3 GPCR / GPCR, family 3, metabotropic glutamate receptor 5 / GPCR, family 3 / Receptor, ligand binding region / GPCR, family 3, nine cysteines domain / G-protein coupled receptors family 3 signature 1. / GPCR, family 3, nine cysteines domain superfamily / G-protein coupled receptors family 3 signature 2. / GPCR family 3, C-terminal / G-protein coupled receptors family 3 signature 3. / G-protein coupled receptors family 3 profile. / G alpha (q) signalling events / Class C/3 (Metabotropic glutamate/pheromone receptors) / Neurexins and neuroligins / 7 transmembrane sweet-taste receptor of 3 GCPR / regulation of translational elongation / phospholipase C-activating G protein-coupled glutamate receptor signaling pathway / G protein-coupled receptor activity involved in regulation of postsynaptic membrane potential / trans-synaptic signaling by endocannabinoid, modulating synaptic transmission / protein tyrosine kinase activator activity / postsynaptic modulation of chemical synaptic transmission / neurotransmitter receptor activity involved in regulation of postsynaptic cytosolic calcium ion concentration / G protein-coupled glutamate receptor signaling pathway / regulation of intracellular calcium activated chloride channel activity / glutamate receptor activity / G protein-coupled receptor activity / postsynaptic density membrane / modulation of age-related behavioral decline / calcium-mediated signaling using intracellular calcium source / protein tyrosine kinase binding / synapse organization / regulation of synaptic transmission, glutamatergic / locomotory behavior / cognition / regulation of protein phosphorylation / learning / Schaffer collateral - CA1 synapse / positive regulation of protein tyrosine kinase activity / regulation of long-term neuronal synaptic plasticity / cellular response to amyloid-beta / learning or memory / regulation of translation / chemical synaptic transmission / neuron projection / G protein-coupled receptor signaling pathway / integral component of plasma membrane / plasma membrane / cytoplasm / Metabotropic glutamate receptor 5
Function and homology information
Specimen sourceHomo sapiens (human)
Lama glama (llama)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / 3.262 Å resolution
AuthorsKoehl, A. / Hu, H. / Feng, D. / Sun, B. / Chu, M. / Weis, W.I. / Mathiesen, J.M. / Skiniotis, G. / Kobilka, B.K.
Funding supportUnited States , 2 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Neurological Disorders and StrokeNS092695United States
National Institutes of Health/National Institute of Neurological Disorders and StrokeNS028471United States
CitationJournal: Nature / Year: 2019
Title: Structural insights into the activation of metabotropic glutamate receptors.
Authors: Antoine Koehl / Hongli Hu / Dan Feng / Bingfa Sun / Yan Zhang / Michael J Robertson / Matthew Chu / Tong Sun Kobilka / Toon Laeremans / Jan Steyaert / Jeffrey Tarrasch / Somnath Dutta / Rasmus Fonseca / William I Weis / Jesper M Mathiesen / Georgios Skiniotis / Brian K Kobilka
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Nov 20, 2018 / Release: Jan 23, 2019
RevisionDateData content typeGroupCategoryItemProviderType
1.0Jan 23, 2019Structure modelrepositoryInitial release
1.1Feb 6, 2019Structure modelData collection / Database referencescitation / citation_author_citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
1.2Feb 20, 2019Structure modelData collection / Database referencescitation_citation.journal_volume / _citation.page_first / _citation.page_last

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Metabotropic glutamate receptor 5
B: Metabotropic glutamate receptor 5
C: Metabotropic glutamate receptor 5
D: Metabotropic glutamate receptor 5
E: Nanobody 43
F: Nanobody 43
G: Nanobody 43
H: Nanobody 43
hetero molecules


Theoretical massNumber of molelcules
Total (without water)327,90233
Polyers323,0018
Non-polymers4,90125
Water0
1
A: Metabotropic glutamate receptor 5
F: Nanobody 43
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,5786
Polyers80,7502
Non-polymers8284
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Metabotropic glutamate receptor 5
E: Nanobody 43
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,28310
Polyers80,7502
Non-polymers1,5328
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Metabotropic glutamate receptor 5
H: Nanobody 43
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,9388
Polyers80,7502
Non-polymers1,1886
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Metabotropic glutamate receptor 5
G: Nanobody 43
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,1039
Polyers80,7502
Non-polymers1,3527
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
γ
α
β
Length a, b, c (Å)95.528, 158.389, 111.963
Angle α, β, γ (deg.)90.000, 101.930, 90.000
Int Tables number4
Space group name H-MP 1 21 1

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Components

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Protein/peptide , 2 types, 8 molecules ABCDEFGH

#1: Protein/peptide
Metabotropic glutamate receptor 5 / / mGluR5


Mass: 67395.633 Da / Num. of mol.: 4 / Source: (gene. exp.) Homo sapiens (human) / Gene: GRM5, GPRC1E, MGLUR5 / Plasmid name: pVL1392 / Cell line (production host): High Five / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P41594
#2: Protein/peptide
Nanobody 43 / Single-domain antibody


Mass: 13354.672 Da / Num. of mol.: 4 / Details: Nanobody 43 / Source: (gene. exp.) Lama glama (llama) / Plasmid name: PET SUMO / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)

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Non-polymers , 4 types, 25 molecules

#3: Chemical
ChemComp-NAG / N-ACETYL-D-GLUCOSAMINE


Mass: 221.208 Da / Num. of mol.: 12 / Formula: C8H15NO6 / N-Acetylglucosamine
#4: Chemical
ChemComp-FUC / ALPHA-L-FUCOSE


Mass: 164.156 Da / Num. of mol.: 6 / Formula: C6H12O5
#5: Chemical ChemComp-BMA / BETA-D-MANNOSE


Mass: 180.156 Da / Num. of mol.: 3 / Formula: C6H12O6
#6: Chemical
ChemComp-MAN / ALPHA-D-MANNOSE


Mass: 180.156 Da / Num. of mol.: 4 / Formula: C6H12O6

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.73 / Density percent sol: 54.9 %
Crystal growTemp: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 18-20% PEG 3350 0.15M Potassium Nitrate 1% Benzamidine

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Data collection

DiffractionMean temperature: 100 kelvins / Serial crystal experiment: N
SourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.97946 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Collection date: May 23, 2016
RadiationDiffraction protocol: SINGLE WAVELENGTH / Monochromatic or laue m l: M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionD resolution high: 3.26 Å / D resolution low: 39.6 Å / Number obs: 49878 / CC half: 0.926 / Rmerge I obs: 0.132 / Rpim I all: 0.083 / Rrim I all: 0.156 / NetI over sigmaI: 7.6 / Number measured all: 174911 / Redundancy: 3.5 % / Scaling rejects: 21 / Percent possible obs: 98.4
Reflection shell

Diffraction ID: 1

Rmerge I obsHighest resolutionLowest resolutionNumber measured allNumber unique obsCC halfRpim I allRrim I allNetI over sigmaI obsRedundancyPercent possible all
0.8193.2603.3701502143890.6460.5120.9691.4003.40094.000
0.04613.05039.60024977780.9820.0320.05622.7003.20094.200

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Processing

Software
NameVersionClassification
PHENIX1.14_3211refinement
XDSdata reduction
Aimless0.5.25data scaling
PDB_EXTRACT3.24data extraction
PHASERphasing
RefineMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3LMK
Overall SU ML: 0.46 / Cross valid method: THROUGHOUT / Sigma F: 1.33 / Overall phase error: 28.09
Solvent computationSolvent shrinkage radii: 0.9 Å / Solvent vdw probe radii: 1.11 Å
Displacement parametersB iso max: 170.07 Å2 / B iso mean: 79.1425 Å2 / B iso min: 34.3 Å2
Least-squares processR factor R free: 0.251 / R factor R work: 0.1993 / R factor obs: 0.2014 / Highest resolution: 3.262 Å / Lowest resolution: 38.87 Å / Number reflection R free: 1999 / Number reflection obs: 49835 / Percent reflection R free: 4.01 / Percent reflection obs: 98.25
Refine hist #finalHighest resolution: 3.262 Å / Lowest resolution: 38.87 Å / B iso mean ligand: 125.39 / Number residues total: 2503
Number of atoms included #finalProtein: 19321 / Nucleic acid: 0 / Ligand: 305 / Solvent: 0 / Total: 19626
Refine LS shell

Refine ID: X-RAY DIFFRACTION / R factor R free error: 0 / Total number of bins used: 14

Highest resolutionR factor R freeR factor R workLowest resolutionNumber reflection R freeNumber reflection R workNumber reflection allPercent reflection obs
3.26250.37800.31013.34401333196332993.0000
3.34400.35960.27693.43441453440358599.0000
3.43440.30800.25573.53541433453359699.0000
3.53540.33030.24113.64941423413355599.0000
3.64940.31860.22913.77971423397353998.0000
3.77970.26670.20843.93091423387352998.0000
3.93090.26430.19704.10961453470361599.0000
4.10960.25790.18354.32601443424356899.0000
4.32600.20620.16214.59671433420356399.0000
4.59670.20870.16134.95091423406354898.0000
4.95090.19930.16635.44791443469361399.0000
5.44790.24030.19176.23351463459360599.0000
6.23350.22310.19987.84291433433357699.0000
7.84290.22250.190738.87301453469361498.0000

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